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czbiohub-sf / tabula-muris-senis

Tabula Muris Senis
http://tabula-muris-senis.ds.czbiohub.org
BSD 3-Clause "New" or "Revised" License
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mislabeling of marrow clusters? #4

Closed swolock closed 4 years ago

swolock commented 5 years ago

Hello,

Thanks for providing what promises to be a great resource! I primarily study hematopoiesis and was quickly checking out your bone marrow droplet data. I noticed that several of the cell_ontology_class labels seem incorrect, at least based on my experience with similar datasets. I suspect the issue is the result of a simple human error in the matching of cell_ontology_class labels with cluster IDs rather than outright misclassification, since some class labels have been assigned to quite unrelated clusters (e.g., "granulocytopoietic cell").

Below is a figure with cells colored by the labels from the h5ad files/cellxgene (left panel, arrows marking labels that I'm confident are incorrect) and by marker gene expression (right panel).

tab_mur_clusts_labeled

If you prefer to receive feedback through other channels, let me know.

Best, Sam

aopisco commented 5 years ago

Hi @swolock I'll check with the tissue expert @transcriptomics and get back to you

aopisco commented 5 years ago

@swolock thanks again for finding this label swap! The correct object is now in figshare. Can you please let me know if you can access it and if it's now consistent with your markers? I'll wait for your reply before closing the issue

aopisco commented 4 years ago

Closing the issue for now, let me know if you find something else

swolock commented 4 years ago

@aopisco Apologies for not getting back to you on this. I quickly checked the new data files, and they look good to me. Thanks!

genecell commented 3 years ago

@aopisco Apologies for not getting back to you on this. I quickly checked the new data files, and they look good to me. Thanks!

Hi @swolock, your cmap colors are beautiful, could you please share your cmap configurations with me, thank you!

swolock commented 3 years ago

Thanks @genecell! If you're referring to the gene expression plots, you can check out this function for plotting multiple genes from an AnnData object. The color map itself is just matplotlib's "Reds" color map that has been made slightly darker – see here.

For the plot of the cell clusters, I think I used "Paired", but I'm not positive.